Drosophila melanogaster vs Drosophila simulans LastZ Results

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Drosophila melanogaster (Drosophila melanogaster, BDGP6) and Drosophila simulans (Drosophila simulans, ASM75419v3) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Metazoa release . Drosophila melanogaster was used as the reference species. After running LastZ, the raw LastZ alignment blocks are chained according to their location in both genomes. During the final netting process, the best sub-chain is chosen in each region on the reference species.

Results

Number of alignment blocks: 59,100

Genome coverage (bp) Coding exon coverage (bp)
Drosophila melanogaster

Uncovered: 25,812,145 out of 143,725,995
Covered: 117,913,850 out of 143,725,995

Uncovered: 183,687 out of 22,848,419
Matches: 21,710,184 out of 22,848,419
Mismatches: 890,951 out of 22,848,419
Insertions: 63,597 out of 22,848,419

Drosophila simulans

Uncovered: 9,649,908 out of 124,963,774
Covered: 115,313,866 out of 124,963,774

Uncovered: 59,594 out of 22,371,299
Matches: 21,364,569 out of 22,371,299
Mismatches: 884,543 out of 22,371,299
Insertions: 62,593 out of 22,371,299

Configuration parameters

ParameterValue
Gap open penalty (O)400
Gap extend penalty (E)30
HSP threshold (K)
Threshold for gapped extension (L)3000
Threshold for alignments between gapped alignment blocks (H)2200
Masking count (M)
Seed and Transition value (T)1
Scoring matrix (Q)
Default:
     A    C    G    T
    91 -114  -31 -123
  -114  100 -125  -31
   -31 -125  100 -114
  -123  -31 -114   91
Other parameters (other)--ambiguous=iupac

Chunking parameters

Drosophila melanogaster Drosophila simulans
Chunk size 10,000,000 10,100,000
Overlap 0 100,000
Group set size 0 10,100,000
Masking options {default_soft_masking => 1} {default_soft_masking => 1}